Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1584 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0522018171 sf0521955613 5 22018171 4.61E-07 4.61E-07
vg1005036154 sf1005052691 10 5036154 6.51E-07 6.51E-07
vg1128801838 sf1128278617 11 28801838 6.91E-07 6.91E-07
vg0719103699 sf0719102706 7 19103699 7.31E-07 7.31E-07
vg0300230192 sf0300229192 3 230192 1.28E-06 1.28E-06
vg1116560090 sf1116094968 11 16560090 1.60E-06 1.60E-06
vg1123916455 sf1123450325 11 23916455 2.38E-06 2.38E-06
vg0414098504 sf0414089219 4 14098504 2.54E-06 2.54E-06
vg0118087044 sf0118085998 1 18087044 3.73E-06 3.73E-06
vg0140618344 sf0140617301 1 40618344 4.64E-06 4.64E-06